Molecular analysis of a California strain of Rupestris stem pitting-associated virus isolated from declining Syrah grapevines

Lima, M. F.; Alkowni, Raed; Uyemoto, J. K.; Golino, Deborah A.; Osman, Fatima; Rowhani, Adib

doi:10.1007/s00705-006-0742-y

Cited by 49 publications

(45 citation statements)

References 9 publications

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“…110R (V. berlandieri x V. rupestris), not inoculated, exhibiting severe vein necrosis on leaves were sampled for total RNA extractions using the RNeasy Plant Mini kit (Qiagen) from 100mg of petioles of symptomatic leaves, grinding plant tissue in liquid nitrogen. Primer pairs used to amplify the partial CP of GRSPaV for one-step RT-PCR were 48V/49C (LIMA et al, 2006). The RT-PCR in a single step was carried out using One Step RT-PCR kit (Qiagen) and reactions were performed according to the manufacturer with 4μL of total RNA (ca.…”

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confidence: 99%

Molecular variants of Grapevine rupestris stem pitting-associated virus infecting grapevines (Vitis spp.) in Brazil

2017

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Variantes moleculares deAmong grapevine (Vitis spp.) pathogens, viruses stand out, considering that this crop is susceptible to numerous graft-transmissible agents that cause several diseases, reducing plant vigor, yield, productivity and also fruit quality. Grapevine rupestris stem pitting-associated virus (GRSPaV), genus Foveavirus, family Betaflexiviridae, is one of the most common viruses of grapevine and is widely distributed in many grape-growing areas of the world. GRSPaV is not mechanically transmissible and natural vectors are unknown. This virus is involved in the rugose wood complex as the agent of the disorder known as Rupestris stem pitting, and some of its strains have been shown to have a very close association with specific symptoms and disorders (BOUYAHIA et al., 2005). Since the characterization of GRSPaV in 1998, a number of studies have revealed the remarkable genetic variability of this virus, which may reflect the unclear pattern of its biological effects (MENG & GONSALVES, 2007). At least, ten GRSPaV variants have been fully sequenced: GRSPaV (GenBank accession AF026278), RSPaV-1 (AF057136), -SG1 (AY881626), -BS (AY881627), -SY (AY368590), -PN (AY368172), -MG (FR691076), -PG (HE591388), -3138-07 (JX559646) and -GG (JQ922417) (HU et al., 2015). They are divided into four main groups depending on their complete genome sequences, and each group has the reference variant lineage (in bold) defined by NOLASCO et al. (2006) or MENG et al. (2006, respectively as follows: GRSPaV-SY and VS (1 or IV), GRSPaV-SG1, MG and 3138- ABSTRACT: Grapevine rupestris stem pitting-associated virus (GRSPaV) is one of the most common viruses of grapevine. It is involved in the grafttransmissible disease rupestris stem pitting of the rugose wood complex. The objective of the research was to perform the molecular characterization of the coat protein (CP) gene of sixteen Brazilian GRSPaV isolates aiming to determine the occurrence of molecular variants (strains) of this virus. Nine grapevine samples were evaluated, from which dsRNA was extracted. Nucleotide sequences were generated by Next generation sequencing (NGS). Fifteen complete sequences of the GRSPaV CP gene were obtained and phylogenetically analyzed. Multiple alignments of the sequences showed identities of nucleotides ranging from 82% to 99%, suggesting high variability among the CPs of Brazilian isolates. The study revealed that genetic variability of GRSPaV comprising three molecular variants is also present in

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confidence: 99%

Molecular variants of Grapevine rupestris stem pitting-associated virus infecting grapevines (Vitis spp.) in Brazil

2017

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“…Estudos adicionais de caracterização biológica necessitariam ser conduzidos neste caso. Os oligonucleotídeos específicos para a estirpe Syrah foram desenhados com base no gene da replicase, numa região que apresenta significativa variabilidade, permitindo assim a diferenciação desta estirpe de outras (LIMA et al, 2006 Ciência Rural, v.40, n.11, nov, 2010.…”

Section: Resultsunclassified

“…Para o GLRaV-2, as estirpes consideradas foram: 93/955, PN (=Sem, 94/970), H4, RG, Alfie e BD (ABOU GHANEM-SABANADZOVIC et al, 2000;BERTAZZON & ANGELINI, 2004;MENG et al, 2005a). Em relação ao RSPaV, foram consideradas as estirpes GRSPaV-VS, GRSPaV-BS, GRSPaV-SG1 e GRSPaV-1 (MENG et al, 2006;ALABI et al, 2010) e Syrah (SY) (LIMA et al, 2006) e Pinot Noir (PN) ), recentemente identificadas. Para o GLRaV-3 foi considerada apenas a estirpe "típica" NY (New York) (LING et al, 1997).…”

Section: (Gva) Grapevine Virus B (Gvb) Grapevine Virus D (Gvd) Graunclassified

Detecção e identificação molecular de vírus associados a videiras sintomáticas e assintomáticas

et al. 2010

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IIDetecção e identificação molecular de vírus associados a videiras sintomáticas e assintomáticas -1 a -4 de Grapevine virus A (GVA), Grapevine virus B (GVB), Grapevine virus D (GVD), Grapevine fleck virus (GFkV), Grapevine fanleaf virus (GFLV), Arabis mosaic virus (ArMV), Grapevine chrome mosaic virus (GCMV), Rupestris stem pitting-associated virus (RSPaV), Grapevine leafroll-associated virus 1 a 4 (GLRaV ABSTRACT The vegetative propagation of grapevine facilitates multiple viral infections, with different symptoms which vary according to combinations of cultivar or host species with viral species. The aims of this research were to detect and identify the viral species infecting two grapevine species/cultivars: one symptomatic and one symptomless. DsRNA from both samples was assayed by RT-PCR using 17 pairs of specific primers for detection of the Grapevine virus A (GVA), Grapevine virus B (GVB), Grapevine virus D (GVD), Grapevine fleck virus (GFkV), Grapevine fanleaf virus (GFLV), Arabis mosaic virus (ArMV), Grapevine chrome mosaic virus (GCMV), Rupestris stem pitting-associated virus (RSPaV) and

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“…Através da análise da identidade de nt desses isolados de RSPaV, pôde-se verificar a formação de quatro agrupamentos distintos, à semelhança de outros trabalhos (Lima et al 2006;Meng et al, 2006;Nolasco et al, 2006;Nakaune et al 2008 1 -Árvores filogenéticas não enraizadas, obtidas com o programa MEGA 4.1, baseadas nas sequências completas de nucleotídeos do gene da proteína capsidial dos isolados de (A) Rupestris stem pitting associated virus, RSPaV, (B) Grapevine leafroll associated virus 2, GLRaV-2 e (C) Grapevine fanleaf virus, GFLV, com a demarcação de distintos grupos, considerando-se os isolados estudados. Valores percentuais de "bootstrap" são mostrados nos ramos.…”

Section: Rspavunclassified

Variabilidade do gene da proteína capsidial de três espécies virais que infectam videiras no Brasil

Radaelli¹,

Fajardo²,

Nickel³

et al. 2009

Trop. plant pathol.

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RESUMOO objetivo deste trabalho foi avaliar a variabilidade de três vírus (Rupestris stem pitting-associated virus -RSPaV, Grapevine leafroll-associated virus 2 -GLRaV-2 e Grapevine fanleaf virus -GFLV) que infectam videiras no Brasil, através da caracterização molecular do gene da proteína capsidial (CP). Foram amplificados fragmentos que compreendem os genes completos da CP de nove isolados de RSPaV (780 pb), seis de GLRaV-2 (597 pb) e três de GFLV (1515 pb) por RT-PCR, utilizando-se oligonucleotídeos específicos para cada espécie viral. Os DNAs amplificados foram clonados e sequenciados. Os isolados de RSPaV foram reunidos em quatro grupos pela análise filogenética das sequências obtidas com valores de identidade de nucleotídeos (nt) que variaram de 81 a 99%. Para GLRaV-2, dois grupos foram definidos a partir das sequências de nt, com valores de identidade que variaram de 88 a 99% e, para GFLV, foram definidos dois grupos, com valores de identidade de nt que variaram de 89 a 98%. Os diferentes isolados das três espécies virais estudadas também foram detectados utilizando-se hibridização com sondas não-radioativas, marcadas com digoxigenina, possibilitando identificar de forma inequívoca as amostras infectadas, independentemente dos isolados virais empregados para síntese das sondas. Palavras-chave: RSPaV, GLRaV-2, GFLV, RT-PCR, Vitis spp., sonda não-radioativa. ABSTRACT Coat protein gene variability of three viral species infecting grapevines in BrazilThe purpose of this study was to evaluate the variability of three viruses (Rupestris stem pitting-associated virus -RSPaV, Grapevine leafroll-associated virus 2 -GLRaV-2 and Grapevine fanleaf virus -GFLV) infecting grapevines in Brazil, through molecular characterization of the coat protein (CP) gene. DNA fragments were amplified comprising the complete CP genes of nine isolates of RSPaV (780 bp), six of GLRaV-2 (597 bp) and three of GFLV (1515 bp) by RT-PCR, using specific primers for each viral species. The amplified DNA fragments were cloned and sequenced. RSPaV isolates were clustered into four groups by phylogenetic analysis of the nucleotide (nt) sequences of the CP gene, showing identity values ranging from 81 to 99%. For GLRaV-2, two groups were defined from nt sequences, with identity values ranging from 88 to 99% and for GFLV, two groups were defined with identity values ranging from 89 to 98%. The isolates of each viral species studied here were detected by non-radioactive probes labeled with digoxigenin, allowing unambiguous identification of infected samples, independent of the isolate used as template for probe synthesis.

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Molecular analysis of a California strain of Rupestris stem pitting-associated virus isolated from declining Syrah grapevines

Cited by 49 publications

References 9 publications

Molecular variants of Grapevine rupestris stem pitting-associated virus infecting grapevines (Vitis spp.) in Brazil

Molecular variants of Grapevine rupestris stem pitting-associated virus infecting grapevines (Vitis spp.) in Brazil

Detecção e identificação molecular de vírus associados a videiras sintomáticas e assintomáticas

Variabilidade do gene da proteína capsidial de três espécies virais que infectam videiras no Brasil

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